Markers + reference

Chaetoceros

9 species · Chaetocerotaceae · Chaetocerotales

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Species 9
Genome length 116–119 kb
Candidate markers 327
Primer pairs 80

Genome-wide nucleotide diversity

Sliding-window nucleotide diversity
Sliding-window nucleotide diversity (π) across the plastome.

Candidate markers

8 hotspot labels from the diversity plot in genomic order, plus the top 8 remaining regions by MarkerSeek score (out of 327 candidates).

Label Region Length (bp) Pi Alignment reliability MarkerSeek score Primer available Action
ycf35 SSC 378 0.1842 1.00 78.9 yes View details
rps16 SSC 237 0.1998 0.99 72.4 yes View details
syfB SSC 2115 0.2532 1.00 78.1 yes View details
ycf89-trnP(ugg) IRa 298 0.2835 0.95 72.2 yes View details
trnP(ugg)-ycf45 LSC 483 0.2760 0.96 79.8 yes View details
rpoC2 LSC 4260 0.2014 0.99 65.4 yes View details
rpoB LSC 4263 0.1621 0.98 65.2 yes View details
ycf41 LSC 321 0.3171 0.98 64.3 yes View details
ycf89 IRb 1026 0.1584 1.00 82.1 yes View details
ycf89 IRa 1026 0.1586 1.00 82.1 yes View details
rns-trnI(gau) IRb 65 0.1603 0.98 80.4 yes View details
trnI(gau)-rns IRa 65 0.1641 0.98 80.4 yes View details
trnS(gcu)-trnD(guc) LSC 60 0.3680 1.00 79.7 yes View details
rpl20 LSC 345 0.1472 1.00 79.3 yes View details
ccs1 SSC 1275 0.1834 0.99 79.1 yes View details
ccsA SSC 939 0.1233 1.00 79.0 yes View details
Candidate markers include all hotspot labels marked in the diversity plot, listed in genomic order, plus the top 10 remaining regions by MarkerSeek score. Primer design is attempted for every listed region. Primer available: yes means at least one valid primer pair was found; no means no valid pair passed screening; NA means primer design was skipped.

Primer pairs

Showing the top 30 of 80 primer pairs (ranked by primer score).

Primer ID Label Forward Reverse Amplicon (bp) Cross-species rate Score
trnS(gcu)-trnD(guc)_p1 trnS(gcu)-trnD(guc) GGGTTCGAATCCCTGTTTCT AGACTCGAACTCGCAACTTC 145–153 1.000 87.4
trnS(gcu)-trnD(guc)_p2 trnS(gcu)-trnD(guc) GGGTTCGAATCCCTGTTTCT GAGACTCGAACTCGCAACTT 146–154 1.000 87.4
trnS(gcu)-trnD(guc)_p3 trnS(gcu)-trnD(guc) GGGTTCGAATCCCTGTTTCT GCGGTGCTCTAACCAATTGA 113–121 1.000 83.7
trnS(gcu)-trnD(guc)_p4 trnS(gcu)-trnD(guc) GGGTTCGAATCCCTGTTTCT GACTGACGAGACTCGAACTC 153–161 1.000 83.5
trnS(gcu)-trnD(guc)_p5 trnS(gcu)-trnD(guc) GGGTTCGAATCCCTGTTTCT GGACTGACGAGACTCGAACT 154–162 1.000 80.9
rpl20_p1 rpl20 AAAAGCTGCAGCAAAACGTT TTAATGTTACAGGAGCGGCC 1276 0.111 44.1
rpl20_p2 rpl20 AAAAAGACAGGCGCAGGTAA TTAATGTTACAGGAGCGGCC 1254 0.111 44.0
rpl20_p3 rpl20 AAAAGCTGCAGCAAAACGTT AGTCTACCATGGACTGCTGT 1213 0.111 43.9
rpl20_p4 rpl20 AAAAAGACAGGCGCAGGTAA AGTCTACCATGGACTGCTGT 1191 0.111 43.8
rpl20_p5 rpl20 CAGTTGATCAAGGGGCTGTT TTAATGTTACAGGAGCGGCC 1689 0.111 43.5
ycf89_p1 ycf89 AAAATGTTGGCCCAACTTGC CATTGCGGAAAATTCCCCAC 2153 0.111 44.1
ycf89_p2 ycf89 AAAATGTTGGCCCAACTTGC TCTCGTACGACTTGCATGTG 1877 0.111 44.0
ycf89_p3 ycf89 AAAATGTTGGCCCAACTTGC TATTGCTCCGTCAGGCTTTC 2176 0.111 44.0
ycf89_p4 ycf89 AAAATGTTGGCCCAACTTGC AGTTGACTTGTCCAACCACC 2359 0.111 43.7
ycf89_p5 ycf89 AAAATGTTGGCCCAACTTGC GTTGACTTGTCCAACCACCT 2358 0.111 43.7
rns-trnI(gau)_p1 rns-trnI(gau) GACTGGGGTGAAGTCGTAAC CTGGGCCATTCTGGATTTGA 199–202 1.000 87.0
rns-trnI(gau)_p2 rns-trnI(gau) GGGGTGAAGTCGTAACAAGG CTGGGCCATTCTGGATTTGA 195–198 1.000 86.1
rns-trnI(gau)_p3 rns-trnI(gau) GTAACCGTACTGGAAGGTGC CTGGGCCATTCTGGATTTGA 176–179 1.000 85.5
rns-trnI(gau)_p4 rns-trnI(gau) TGACTGGGGTGAAGTCGTAA CTGGGCCATTCTGGATTTGA 200–203 1.000 85.3
rns-trnI(gau)_p5 rns-trnI(gau) AGGTAACCGTACTGGAAGGT CTGGGCCATTCTGGATTTGA 178–181 1.000 85.2
ycf35_p1 ycf35 CCTCCTGGGAAGATAGCTCA AACCTTCGGAAACAGTTGCT 1115 0.111 43.3
ycf35_p2 ycf35 ACCTCCTGGGAAGATAGCTC AACCTTCGGAAACAGTTGCT 1116 0.111 43.3
ycf35_p3 ycf35 GACCTCCTGGGAAGATAGCT AACCTTCGGAAACAGTTGCT 1117 0.111 43.3
ycf35_p4 ycf35 CCTCCTGGGAAGATAGCTCA TGGAGCCCGTCAACTAGTTA 1655 0.111 43.1
ycf35_p5 ycf35 ACCTCCTGGGAAGATAGCTC TGGAGCCCGTCAACTAGTTA 1656 0.111 43.1
rps16_p1 rps16 TCGTTCCCATTCCAAGCAAA TGGAGCCCGTCAACTAGTTA 912 0.111 43.8
rps16_p2 rps16 TTCGTTCCCATTCCAAGCAA TGGAGCCCGTCAACTAGTTA 913 0.111 43.8
rps16_p3 rps16 TCGTTCCCATTCCAAGCAAA AAAAGATCGTCCAGGTCAGC 1155 0.111 43.5
rps16_p4 rps16 TTCGTTCCCATTCCAAGCAA AAAAGATCGTCCAGGTCAGC 1156 0.111 43.5
rps16_p5 rps16 GGGCATGATTGTTCCCAGAA TGGAGCCCGTCAACTAGTTA 957 0.111 42.7

Result downloads

candidate_marker_features.tsv primers.tsv

Reference species (9)

One GenBank record per species. Use the NCBI button to open the Nucleotide entry for the listed accession.

Species Accession Length (bp) Link
Chaetoceros costatus MW845775.1 116845 View on NCBI ↗
Chaetoceros curvisetus MW845780.1 118222 View on NCBI ↗
Chaetoceros laevisporus MW845779.1 119034 View on NCBI ↗
Chaetoceros muelleri NC_053621.1 116284 View on NCBI ↗
Chaetoceros neogracilis MZ352931.1 116421 View on NCBI ↗
Chaetoceros pseudocurvisetus MW845777.1 118127 View on NCBI ↗
Chaetoceros simplex NC_025310.1 116459 View on NCBI ↗
Chaetoceros socialis MW845776.1 117717 View on NCBI ↗
Chaetoceros tenuissimus LC537471.1 116465 View on NCBI ↗